CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = P258P

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
N	258	P258P		syn	ccT	ccC	683	563	0.824305	29045-29047
N	258	P258P		syn	ccT	ccG	683	67	0.0980966	29045-29047
N	258	P258P		syn	ccT	ccA	683	53	0.0775988	29045-29047

Details of the mutation P258P within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORF	CodonNum	Mut	RefCodon	MutCodon	CodonCount	AACount	Lineage	LineageCodonProp
N	258	P258P	ccT	ccC	563	683	All	0.000108
N	258	P258P	ccT	ccG	67	683	All	0.000013
N	258	P258P	ccT	ccA	53	683	All	0.00001
N	258	P258P	ccT	ccC	168	174	B.1.429	0.003953
N	258	P258P	ccT	ccA	6	174	B.1.429	0.000141
N	258	P258P	ccT	ccC	120	120	B.1.1.294	0.151899
N	258	P258P	ccT	ccC	44	45	AY.44	0.000268
N	258	P258P	ccT	ccG	1	45	AY.44	0.000006
N	258	P258P	ccT	ccC	28	45	B.1.1.7	0.000025
N	258	P258P	ccT	ccA	14	45	B.1.1.7	0.000013
N	258	P258P	ccT	ccG	3	45	B.1.1.7	0.000003
N	258	P258P	ccT	ccC	43	43	M.1	1
N	258	P258P	ccT	ccG	17	17	AY.3	0.000169
N	258	P258P	ccT	ccG	14	14	B.1.351	0.000416
N	258	P258P	ccT	ccC	12	14	B.1.617.2	0.000045
N	258	P258P	ccT	ccA	2	14	B.1.617.2	0.000008
N	258	P258P	ccT	ccC	11	13	B.1	0.000101
N	258	P258P	ccT	ccG	2	13	B.1	0.000018
N	258	P258P	ccT	ccC	13	13	B.1.632	0.087248
N	258	P258P	ccT	ccG	12	12	AY.26	0.00034
N	258	P258P	ccT	ccC	6	12	AY.4	0.000009
N	258	P258P	ccT	ccG	5	12	AY.4	0.000008
N	258	P258P	ccT	ccA	1	12	AY.4	0.000002
N	258	P258P	ccT	ccC	10	11	AY.43	0.000044
N	258	P258P	ccT	ccG	1	11	AY.43	0.000004
N	258	P258P	ccT	ccA	6	8	AY.5	0.000124
N	258	P258P	ccT	ccC	2	8	AY.5	0.000041
N	258	P258P	ccT	ccC	8	8	B.1.400	0.003432
N	258	P258P	ccT	ccC	8	8	B.1.480	0.0199
N	258	P258P	ccT	ccG	3	6	AY.20	0.000117
N	258	P258P	ccT	ccC	3	6	AY.20	0.000117
N	258	P258P	ccT	ccA	3	6	B.1.2	0.000026
N	258	P258P	ccT	ccG	2	6	B.1.2	0.000018
N	258	P258P	ccT	ccC	1	6	B.1.2	0.000009
N	258	P258P	ccT	ccC	6	6	B.1.427	0.000303
N	258	P258P	ccT	ccA	6	6	P.1	0.000095
N	258	P258P	ccT	ccC	5	5	AY.29	0.000079
N	258	P258P	ccT	ccC	5	5	AY.29.1	0.001103
N	258	P258P	ccT	ccA	2	5	AY.39	0.000049
N	258	P258P	ccT	ccC	2	5	AY.39	0.000049
N	258	P258P	ccT	ccG	1	5	AY.39	0.000025
N	258	P258P	ccT	ccC	3	5	B.1.36.29	0.001552
N	258	P258P	ccT	ccG	2	5	B.1.36.29	0.001035
N	258	P258P	ccT	ccC	5	5	B.1.469	0.018051
N	258	P258P	ccT	ccC	4	4	AY.102	0.000106
N	258	P258P	ccT	ccA	4	4	B.1.258.17	0.000416
N	258	P258P	ccT	ccC	3	3	AY.103	0.000019
N	258	P258P	ccT	ccC	3	3	AY.25	0.000018
N	258	P258P	ccT	ccA	3	3	AY.98.1	0.000145
N	258	P258P	ccT	ccC	3	3	B.1.177.57	0.000843
N	258	P258P	ccT	ccC	3	3	B.1.369	0.000856
N	258	P258P	ccT	ccC	2	2	AY.47	0.000062
N	258	P258P	ccT	ccC	2	2	AY.93	0.000546
N	258	P258P	ccT	ccC	2	2	B.1.1	0.000036
N	258	P258P	ccT	ccA	2	2	B.1.1.70	0.000682
N	258	P258P	ccT	ccC	2	2	B.1.177	0.000026
N	258	P258P	ccT	ccC	2	2	B.1.177.86	0.000367
N	258	P258P	ccT	ccC	2	2	B.1.258	0.000133
N	258	P258P	ccT	ccA	2	2	B.1.564.1	0.003155
N	258	P258P	ccT	ccC	2	2	B.1.621	0.000177
N	258	P258P	ccT	ccC	2	2	C.1	0.004785
N	258	P258P	ccT	ccC	1	1	AY.100	0.000046
N	258	P258P	ccT	ccC	1	1	AY.116	0.000287
N	258	P258P	ccT	ccC	1	1	AY.120	0.000037
N	258	P258P	ccT	ccC	1	1	AY.120.2	0.001285
N	258	P258P	ccT	ccC	1	1	AY.13	0.000161
N	258	P258P	ccT	ccC	1	1	AY.16.1	0.00047
N	258	P258P	ccT	ccC	1	1	AY.23	0.00007
N	258	P258P	ccT	ccC	1	1	AY.27	0.000065
N	258	P258P	ccT	ccC	1	1	AY.34	0.000097
N	258	P258P	ccT	ccG	1	1	AY.36	0.000148
N	258	P258P	ccT	ccA	1	1	AY.4.2	0.000022
N	258	P258P	ccT	ccC	1	1	AY.46	0.000104
N	258	P258P	ccT	ccC	1	1	AY.57	0.000656
N	258	P258P	ccT	ccC	1	1	AY.6	0.000041
N	258	P258P	ccT	ccC	1	1	AY.71	0.000475
N	258	P258P	ccT	ccC	1	1	AY.74	0.000116
N	258	P258P	ccT	ccG	1	1	AY.85	0.000427
N	258	P258P	ccT	ccC	1	1	AY.9	0.000068
N	258	P258P	ccT	ccG	1	1	AY.9.2	0.000037
N	258	P258P	ccT	ccC	1	1	B.1.1.337	0.003597
N	258	P258P	ccT	ccC	1	1	B.1.157	0.002985
N	258	P258P	ccT	ccC	1	1	B.1.177.55	0.002331
N	258	P258P	ccT	ccC	1	1	B.1.336	0.002439
N	258	P258P	ccT	ccC	1	1	B.1.36.10	0.004785
N	258	P258P	ccT	ccC	1	1	B.1.36.39	0.002217
N	258	P258P	ccT	ccC	1	1	B.1.39	0.003906
N	258	P258P	ccT	ccC	1	1	B.1.441	0.009615
N	258	P258P	ccT	ccC	1	1	B.1.538	0.008065
N	258	P258P	ccT	ccA	1	1	B.1.618	0.004032
N	258	P258P	ccT	ccC	1	1	B.1.623	0.000536
N	258	P258P	ccT	ccC	1	1	C.37	0.000116
N	258	P258P	ccT	ccC	1	1	N.4	0.004255
N	258	P258P	ccT	ccG	1	1	P.1.1	0.000318
N	258	P258P	ccT	ccC	1	1	P.1.7	0.000319

CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.